r - How to change the figure caption format in bookdown

Question

When using bookdown (single document), figures are numbered automatically as:

Figure 1 Text of figure caption.

In chemistry, the convention is to label main Figures as:

Figure 1. Text of figure caption.

and for the supporting information document:

Figure S1. Text of figure caption.

Also in the figure reference in the text we need:

...as can be seen in Figure 1, ...

so the reference text should not be bold.

Question

How can i make bookdown (or rmarkdown) produce figure and table captions like so: "Figure S1. Some text." and "Table S1. Some text." ?

I need this to be in MS Word format.

Example/ Attempted Solution

So far i tried to modify the _bookdown.yml document as follows:

language:
  label:
    fig: "**Figure S**"
    tab: "**Table S**"

This gives: Figure S1 Some text... and the inline reference when using:

Figure S@ref(fig:Xray)

is Figure S1 which is ok.

Here is a minimal example:

---
title: Supporting Information
subtitle: "Iron(I) etc"
author: "Some people here"
abstract: "Added the addresses here since there is no abstract in the SI"
output:
  bookdown::word_document2:
    fig_caption: yes
    toc: yes
    toc_depth: 1
---

## Reaction of etc.
Some text  (Figure S@ref(fig:Xray)). Some text followed by a figure:

```{r Xray, fig.cap="Single-crystal X-ray structure of some text", echo=FALSE}
plot(cars)
```
Some text etc. followed by a table:

```{r DipUVvis, echo=FALSE, tab.cap="Table caption"}
df<-data.frame(Entry=c('AMM 51$3^a$','AMM 52^*a*^'),
               Precat=c('[FeBr~2~(dpbz)~2~] (4.00)','[FeBr~2~(dpbz)~2~] 
(2.00)'))

kable(head(df), format = "markdown")
```

The code above produces Figure S1 in the figure caption but NOT Figure S1. (Note it is all bold and a full stop in the end).

Answer 1

To my knowledge, you cannot control figure/table captions to do what you want with rmarkdown/bookdown. You can use the package captioner to achieve it, with a catch: it works fine with rmarkdown outputs, but you'll need to do post-processing with bookdown outputs. Here is the Rmd file that produces your desired caption style:

---
title: Supporting Information
subtitle: "Iron(I) etc"
author: "Some people here"
abstract: "Added the addresses here since there is no abstract in the SI"
output:
  word_document:
    fig_caption: yes
---

```{r, include=F}
library(captioner)
tables <- captioner(prefix = "Table S", suffix = ". ", style="b", style_prefix=TRUE, auto_space = FALSE)
figures <- captioner(prefix = "Figure S", suffix = ". ", style="b", style_prefix=TRUE, auto_space = FALSE)

figures("Xray1", "Single-crystal X-ray structure of some text (1)", display=FALSE)
figures("Xray2", "Single-crystal X-ray structure of some text (2)", display=FALSE)
figures("Xray3", "Single-crystal X-ray structure of some text (3)", display=FALSE)
```

## Reaction of etc.
Some text. Some text followed by `r figures("Xray1", display="cite")`, which is the same figure as  `r figures("Xray3", display="cite")` but comes after `r figures("Xray2", display="cite")`.

```{r Xray, fig.cap=figures("Xray1"), echo=FALSE}
plot(cars)
```

```{r Xray2, fig.cap=figures("Xray2"), echo=FALSE}
plot(cars)
```

```{r Xray3, fig.cap=figures("Xray3"), echo=FALSE}
plot(cars)
```

Some text etc. followed by `r tables("tab-DipUVvis", display="cite")`:

```{r DipUVvis, echo=FALSE}
df<-data.frame(Entry=c('AMM 51$3^a$','AMM 52^*a*^'),
               Precat=c('[FeBr~2~(dpbz)~2~] (4.00)','[FeBr~2~(dpbz)~2~] 
(2.00)'))

knitr::kable(head(df), caption=tables("tab-DipUVvis", "Table Caption"))
```

However, if you switch to use bookdown::word_document2 output, the figure caption becomes "Figure 1: Figure S1. ...". I haven't found a way to suppress "Figure 1:" and have to do post-processing in my output to search and replace all "Figure ?:" with "".